Add reference state profile plots to docs

CliMA · Jul 20, 2021 · d61c3cb · d61c3cb
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diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,5 +1,9 @@
 [deps]
+ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DocumenterCitations = "daee34ce-89f3-4625-b898-19384cb65244"
+Glob = "c27321d9-0574-5035-807b-f59d2c89b15c"
+JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 TurbulenceConvection = "8e072fc4-01f8-44fb-b9dc-f9336c367e6b"
diff --git a/docs/make.jl b/docs/make.jl
@@ -1,11 +1,17 @@
 using TurbulenceConvection, Documenter
 using DocumenterCitations
+import Glob
+
+# https://github.com/jheinen/GR.jl/issues/278#issuecomment-587090846
+ENV["GKSwstype"] = "nul"
 
 bib = CitationBibliography(joinpath(@__DIR__, "bibliography.bib"))
 
 #! format: off
 pages = Any[
     "Home" => "index.md",
+    "Reference states" => "ReferenceStates.md",
+    "References" => "References.md",
 ]
 
 mathengine = MathJax(Dict(
@@ -41,3 +47,16 @@ deploydocs(
     devbranch = "main",
     forcepush = true,
 )
+
+# Clean up
+build_dir = joinpath(@__DIR__, "build")
+if isdir(build_dir)
+    cd(build_dir) do
+        for filename in Glob.glob("Output.*")
+            rm(filename; force = true, recursive = true)
+        end
+        for filename in Glob.glob("*.in")
+            rm(filename; force = true)
+        end
+    end
+end
diff --git a/docs/src/ReferenceStates.md b/docs/src/ReferenceStates.md
@@ -0,0 +1,109 @@
+# Reference States
+
+```@example
+import TurbulenceConvection
+using Plots
+using NCDatasets
+tc_dir = dirname(dirname(pathof(TurbulenceConvection)))
+include(joinpath(tc_dir, "integration_tests", "utils", "generate_namelist.jl"))
+include(joinpath(tc_dir, "integration_tests", "utils", "generate_paramlist.jl"))
+include(joinpath(tc_dir, "integration_tests", "utils", "Cases.jl"))
+using .NameList
+using .ParamList
+import .Cases
+function export_ref_profile(case_name::String)
+    namelist = default_namelist(case_name)
+    paramlist = default_paramlist(case_name)
+    grid = TurbulenceConvection.Grid(namelist)
+    ref_state = TurbulenceConvection.ReferenceState(grid)
+    Stats = TurbulenceConvection.NetCDFIO_Stats(namelist, paramlist, grid)
+    case = Cases.CasesFactory(namelist, paramlist, grid, ref_state)
+    Cases.initialize_reference(case, grid, ref_state, Stats)
+    Dataset(joinpath(Stats.path_plus_file), "r") do ds
+        zc = ds.group["profiles"]["z_half"][:]
+        zf = ds.group["profiles"]["z"][:]
+        ρc_0 = ds.group["reference"]["rho0_half"][:]
+        pc_0 = ds.group["reference"]["p0_half"][:]
+        αc_0 = ds.group["reference"]["alpha0_half"][:]
+        ρf_0 = ds.group["reference"]["rho0"][:]
+        pf_0 = ds.group["reference"]["p0"][:]
+        αf_0 = ds.group["reference"]["alpha0"][:]
+        p1 = plot(ρc_0, zc ./ 1000;label="centers")
+        plot!(ρf_0, zf ./ 1000;label="faces")
+        plot!(size=(1000,400))
+        plot!(margin=5Plots.mm)
+        xlabel!("ρ_0")
+        ylabel!("z (km)")
+        title!("ρ_0")
+
+        p2 = plot(pc_0 ./ 1000, zc ./ 1000;label="centers")
+        plot!(pf_0 ./ 1000, zf ./ 1000;label="faces")
+        plot!(size=(1000,400))
+        plot!(margin=5Plots.mm)
+        xlabel!("p_0 (kPa)")
+        ylabel!("z (km)")
+        title!("p_0 (kPa)")
+
+        p3 = plot(αc_0, zc ./ 1000;label="centers")
+        plot!(αf_0, zf ./ 1000;label="faces")
+        plot!(size=(1000,400))
+        plot!(margin=5Plots.mm)
+        xlabel!("α_0")
+        ylabel!("z (km)")
+        title!("α_0")
+
+        plot(p1,p2,p3; layout=(1,3))
+        savefig("$case_name.svg")
+    end
+end
+for case_name in (
+    "Bomex",
+    "life_cycle_Tan2018",
+    "Soares",
+    "Rico",
+    "TRMM_LBA",
+    "ARM_SGP",
+    "GATE_III",
+    "DYCOMS_RF01",
+    "GABLS",
+    "SP",
+    "DryBubble",
+)
+    export_ref_profile(case_name)
+end;
+```
+
+## Bomex
+![](Bomex.svg)
+
+## life\_cycle\_Tan2018
+![](life_cycle_Tan2018.svg)
+
+## Soares
+![](Soares.svg)
+
+## Rico
+![](Rico.svg)
+
+## TRMM\_LBA
+![](TRMM_LBA.svg)
+
+## ARM\_SGP
+![](ARM_SGP.svg)
+
+## GATE\_III
+![](GATE_III.svg)
+
+## DYCOMS\_RF01
+![](DYCOMS_RF01.svg)
+
+## GABLS
+![](GABLS.svg)
+
+## SP
+![](SP.svg)
+
+## DryBubble
+![](DryBubble.svg)
+
+
diff --git a/docs/src/References.md b/docs/src/References.md
@@ -0,0 +1,5 @@
+# References
+
+```@bibliography
+```
+